+Open data
-Basic information
Entry | Database: PDB / ID: 1bmf | ||||||
---|---|---|---|---|---|---|---|
Title | BOVINE MITOCHONDRIAL F1-ATPASE | ||||||
Components | (BOVINE MITOCHONDRIAL F1- ...) x 3 | ||||||
Keywords | ATP PHOSPHORYLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | ||||||
Authors | Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E. | ||||||
Citation | Journal: Nature / Year: 1994 Title: Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Authors: Abrahams, J.P. / Leslie, A.G. / Lutter, R. / Walker, J.E. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / Walker, J.E. #2: Journal: Embo J. / Year: 1993 Title: Inherent Asymmetry of the Structure of F1-ATPase from Bovine Heart Mitochondria at 6.5 A Resolution Authors: Abrahams, J.P. / Lutter, R. / Todd, R.J. / Van Raaij, M.J. / Leslie, A.G. / Walker, J.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bmf.cif.gz | 583.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bmf.ent.gz | 471.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/1bmf ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bmf | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-BOVINE MITOCHONDRIAL F1- ... , 3 types, 7 molecules ABCDEFG
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P19483, EC: 3.6.1.34 #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P00829, EC: 3.6.1.34 #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34 |
---|
-Non-polymers , 4 types, 613 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ANP / #6: Chemical | ChemComp-ADP / | #7: Water | ChemComp-HOH / | |
---|
-Details
Compound details | THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE ...THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE NON-CATALYTIC ALPHA SUBUNIT AND THREE COPIES OF THE CATALYTIC BETA SUBUNIT. IN THE PRIMARY REFERENCE, THE BETA SUBUNITS WERE LABELED ACCORDING TO THE BOUND NUCLEOTIDE |
---|---|
Nonpolymer details | CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN ...CRYSTALS WERE GROWN IN THE PRESENCE OF AZIDE, A KNOWN INHIBITOR, BUT THIS HAS NOT BEEN LOCATED IN THE STRUCTURE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 17 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.2 / Details: pH 8.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-24 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 269 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.85 Å / Num. obs: 96689 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.098 |
Reflection shell | Highest resolution: 2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.19 / % possible all: 92 |
Reflection | *PLUS Highest resolution: 2.85 Å / Num. all: 96689 / % possible obs: 97.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 92 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: CCP4 Resolution: 2.85→6 Å / σ(F): 0 Details: RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. THE POSITIONS OF SIDE CHAIN ATOMS WITH TEMPERATURE FACTORS ...Details: RESIDUES B 402 - B 409 INCLUSIVE HAVE BEEN GIVEN ZERO OCCUPANCY AS THERE WAS NO INTERPRETABLE ELECTRON DENSITY IN THIS REGION. THE POSITIONS OF SIDE CHAIN ATOMS WITH TEMPERATURE FACTORS GREATER THAN 75 IS UNCERTAIN. THE MAIN CHAIN CONFORMATION IS ALSO UNCERTAIN FOR REGIONS WITH TEMPERATURE FACTORS ABOVE 60. SOLVENT MOLECULES HAVE BEEN USED TO MODEL SOME FEATURES IN THE ELECTRON DENSITY THAT ARE PROBABLY DUE TO THE "MISSING" REGIONS OF THE GAMMA SUBUNIT (CHAIN G) THE PEPTIDE BOND BETWEEN ASP 269 AND ASP 270 IN CHAINS A, B, C AND THE PEPTIDE BOND BETWEEN ASP 256 AND ASN 257 IN CHAINS D, E, AND F HAVE BEEN MODELED IN A CIS CONFORMATION. RESIDUAL FEATURES IN THE ELECTRON DENSITY MAP SUGGEST THAT THERE IS SOME CONFORMATIONAL DISORDER IN ASP 270 IN CHAINS A, B, AND C.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.85 Å / Lowest resolution: 6 Å / Num. reflection obs: 86186 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.172 / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|